A Dutch woman who has lived in the UK for 24 years, and has two children with her British husband, has been told by the Home Office that she should make arrangements to leave the country after she applied for citizenship after the EU referendum.

The story of Monique Hawkins highlights the practical difficulties faced by millions of EU citizens concerned that they will not have the right to stay in Britain post-Brexit.

Hawkins had considered applying for citizenship before but decided not to as it did not confer any rights beyond her current EU rights. However, after the referendum she changed her mind, fearful that those rights would be diminished after Britain leaves the EU.

European citizens marrying Britons do not automatically qualify for UK citizenship under current rules and Hawkins was concerned that if she did not apply she would be forced “to join a US-style two-hour immigration queue” while the rest of her family “sail through the UK passport lane”.

Hawkins said the Home Office had overlooked vital information in her submission – she was unable to supply an original of her Dutch passport because her father had recently died and she needed her passport to continue to travel to the Netherlands to support her mother.

However, the department not only rejected her application but sent her a letter which took no account of her right to be in the country irrespective of their decision. “As you appear to have no alternative basis of stay in the United Kingdom you should now make arrangements to leave,” the letter said.

When she phoned the Home Office to discuss the decision communicated to her in October, four months after her application, she was told her case could not be discussed on the phone or by email. Hawkins said her treatment by the Home Office was as absurd as a “Monty Python” sketch.

In a written complaint, Hawkins said the worst aspect about the process was the inability to contact anyone. She wrote: “I do not believe there is any other business, organisation or even legal process in the world that would treat its customers/clients/applicants in this manner.”

The software engineer, from Surrey, said she never once thought she would be deported but said her experience highlights the absurdity of the Home Office permanent residency process.

She was told that under the rules she could not talk to anyone about her case and after making her written complaint she received a letter saying her complaint did not qualify as a complaint under Home Office guidelines.

She also protested that while the Home Office would not discuss her case with her personally, it was willing to respond to her MP Dominic Raab, who intervened on her behalf.

She has now written to appeal, but says in her complaint: “I am now left totally in limbo. I do not know how long to wait for a reply. I do not know whether my application will be reopened or not.”

She was told the reason for the rejection was because she had not included her original passport.

In her complaint, Hawkins points out that she included a solicitor-approved photocopy of her passport – which is permissible under the rules – plus a covering letter to explain why she could not be without her passport for the four to six months it takes to process.

She said the application form included a box for reasons for not including a valid passport as long as it was due to circumstances beyond your control. “Clearly my father dying did not qualify in the Home Office’s eyes as beyond my control,” said Hawkins.

Hawkins’s complaint also states that her covering letter for her original application said that she would provide her original passport once the case worker assigned to it needed to see it.

Hawkins, who is a software developer and the daughter of a former oil company executive, lived in several countries as a child and says the UK is the only place she feels she can call home. She studied maths at Cambridge University and settled in the UK in 1992. She lives in Surrey and has two children, aged 15 and 17. “I always used to feel I had no roots. Because of my dad’s background we used to move every five years. This is the first time I’ve laid down roots,” she said.

“I had a massive shock following the referendum. I felt very stressed and suddenly felt walking down the street that the place didn’t want me any more. That feeling began to subside, but I thought I should apply for citizenship.”

The application form, which includes a “flummoxing” requirement to list every absence from the UK in the past 24 years, took an entire weekend to complete, she said. “It is important to realise that in applying for permanent residency I am not gaining a right, I am only getting a document stating a right I already have,” she said.

Her husband, Robert, raised another issue: that Europeans married to Britons do not have an automatic right to citizenship. “As a British citizen, I had the expectation that marrying someone from abroad would automatically give them the right to become a British citizen. That seems to be the case unless your wife happens to come from the European Union,” he said.

Hawkins, who has resubmitted an application for permanent residency, said she believed her case drew attention to the “discrimination against EU/UK marriages”. The British spouse cannot sponsor their EU partner and the EU spouse has to apply on their own merits. If they have not worked and are supported by their spouse, they may not meet the selection criteria.